ArticleNature biotechnology2022
Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
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113 citing papers in PubMed, 144 citations in OpenAlex.
- Review
- Decoding chromosome organization using proximity labeling and long-read sequencing.Journal of genetics and genomics = Yi chuan xue bao · 2026Article
- Identification of differential topologically associating domains from low sequencing depth and pseudobulk chromatin contact maps.Genome research · 2026Article
- Unraveling the lexicon of complex mutational phenomena in human cancers.Nature cancer · 2026Review
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human.NAR genomics and bioinformatics · 2026Article
- From field to genome: non-lethal, on-site nanopore-only assembly of the endangered Grenada Frog (Pristimantis euphronides).BMC genomics · 2026Article
- Assessing resistome host range across water reclamation in three geographically distinct communities using Hi-C sequencing.Applied and environmental microbiology · 2026Article
- Conservation of Long G4-rich (LG4) genomic enhancer regulations.BMC genomics · 2026Article
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- Genome assembly of Astatotilapia latifasciata uncovers B chromosome-linked chromatin reorganization.Heredity · 2026Article
- Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).Nature protocols · 2026Review
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- Influence ofGenome research · 2026Article
- Single-molecule nucleosome spacing coordinates chromatin fiber interactions.bioRxiv : the preprint server for biology · 2026Article
- Article
- A chromosome-level genome assembly of the native populations of the Japanese pavement ant, Tetramorium tsushimae Emery (Hymenoptera: Formicidae).Scientific data · 2026Article
- First reference genome for the family Disteniidae (Coleoptera: Chrysomeloidea), the sister lineage to all longhorned beetles (Cerambycidae).Scientific data · 2026Article
- LINE-1 Locus Transcription Nucleates Oncogenic Chromatin Architecture.Cancer discovery · 2026Article
- Article
53 more citing papers are in PubMed but not listed here.
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Authors and funding
24 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-order three-dimensional (3D) interactions between more than two genomic loci are common in human chromatin, but their role in gene regulation is unclear. Previous high-order 3D chromatin assays either measure distant interactions across the genome or proximal interactions at selected targets. To address this gap, we developed Pore-C, which combines chromatin conformation capture with nanopore sequencing of concatemers to profile proximal high-order chromatin contacts at the genome scale. We also developed the statistical method Chromunity to identify sets of genomic loci with frequencies of high-order contacts significantly higher than background ('synergies'). Applying these methods to human cell lines, we found that synergies were enriched in enhancers and promoters in active chromatin and in highly transcribed and lineage-defining genes. In prostate cancer cells, these included binding sites of androgen-driven transcription factors and the promoters of androgen-regulated genes. Concatemers of high-order contacts in highly expressed genes were demethylated relative to pairwise contacts at the same loci. Synergies in breast cancer cells were associated with tyfonas, a class of complex DNA amplicons. These results rigorously link genome-wide high-order 3D interactions to lineage-defining transcriptional programs and establish Pore-C and Chromunity as scalable approaches to assess high-order genome structure.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.